import sys
from collections import *
import csv
import copy
import networkx as nx
import json
from networkx.readwrite import json_graph

IdDict = defaultdict()#Gives you the ID number with a gene input
GeneDict = defaultdict()#gives you a gene with ID number input
AlreadyCreated = set()#All the nodes created in the graph
graph = nx.Graph() # creates the graph object in NetworkX

def Read_And_Generate_Graph_Object():
    FileReader = open('../data/PPI_File.csv')
    readObject = csv.reader(FileReader, delimiter = ',')
    for x in xrange(0, 8):
        next(readObject) # skips first line
    #reads and scans file, creating dictionary
    ReactionGeneDictionary = defaultdict(set) # holds all the matches and type of reaction two genes have
    OutlierList = Create_Outliers_List()
    IDNum = 0 # id num
    for row in readObject: # reads through and fills accordingly
        gene1 = row[0] # The first gene
        gene2 = row[2] # the second gene
        value = row[4] # the kind of reaction it is (ex. PPI)
	if ((gene1 not in AlreadyCreated) and (gene1 not in OutlierList)):
	    graph.add_node(IDNum,label=str(gene1),type="gene") # creates the respective node
	    AlreadyCreated.add(gene1)
	    IdDict[gene1] = IDNum
	    GeneDict[IDNum] = gene1
	    IDNum += 1
	if ((gene2 not in AlreadyCreated) and (gene2 not in OutlierList)):
	    graph.add_node(IDNum,label=str(gene2),type="gene") # creates the respective node
	    AlreadyCreated.add(gene2)
	    IdDict[gene2] = IDNum
	    GeneDict[IDNum] = gene2
	    IDNum += 1
        ReactionGeneDictionary[gene1].add(gene2)
    made = set()
    keyList = ReactionGeneDictionary.keys()
    for key in keyList: #creates all the edges
        for otherGene in ReactionGeneDictionary[key]:
            if((otherGene in AlreadyCreated) and (key in AlreadyCreated)):
                graph.add_edge(IdDict[key], IdDict[otherGene])
                made.add((IdDict[key], IdDict[otherGene]))			
    # gmlFile = open("CheckIt.gml", 'w')
    # nx.write_gml(graph, gmlFile)
    # gmlFile.close()

#reads in an puts into a list the outliers of the data source
def Create_Outliers_List():
    tempListOfGenes=[]
    try:
        FileReader = open("../data/OutlierGenes.txt", 'r')
        #reads and scans file, creating dictionary
        for row in FileReader: # reads thro=ugh and fills accordingly
            tempListOfGenes.append(row.strip("\n"))
            
        FileReader.close()
    except IOError:   
	variable=0	   
    return tempListOfGenes

#generates the shortest paths between two genes
def Create_Path_Shortest(geneOI1, geneOI2):
    geneList = []
    tempone = temptwo = -1
    try: # try except used to prevent breaking of program
        tempone = IdDict[geneOI1]
    except KeyError:
        print "\n" + geneOI1 + " is not in this data source."
    try: # try except used to prevent breaking of program
        temptwo = IdDict[geneOI2]
    except KeyError:
        print "\n" + geneOI2 + " is not in this data source."
    if(tempone >= 0 and temptwo >= 0):
        try: # using try to prevent crashes
            pathlist = nx.all_shortest_paths(graph, tempone, temptwo) # obtains the pathways and creates a list of genes
            for path in pathlist:
                templist = []
		for node in path:
                    templist.append(GeneDict[node])
		geneList.append(templist)
		print templist
        except nx.NetworkXException:
            print ("\nNo path exists between given genes.")
    return geneList
	
def Create_Path_Shortest_With_Key(gene1, gene2, key):
    length = 0	
    
    section1 = nx.shortest_path_length(graph, gene1, IdDict[key])
    section2 = nx.shortest_path_length(graph, gene2, IdDict[key])
    length = section1+section2
    
    return length

#creates paths between two genes given a maximum path length	
def Create_Path_Given_Length(geneOI1, geneOI2, n):
    geneList = []
    tempone = temptwo = -1
    try: # try except used to prevent breaking of program
        tempone = IdDict[geneOI1]
    except KeyError:
        print "\n" + geneOI1 + " is not in this data source."
    try: # try except used to prevent breaking of program
        temptwo = IdDict[geneOI2]
    except KeyError:
        print "\n" + geneOI2 + " is not in this data source."
    if(tempone >= 0 and temptwo >= 0):
        try: # using try to prevent crashes
            size = nx.shortest_path_length(graph, tempone, temptwo) # obtains the pathways and creates a list of genes
            pathlist = nx.all_simple_paths(graph, tempone, temptwo, size+n) # obtains the pathways and creates a list of genes
            for path in pathlist:
                templist = []
                for node in path:
                    templist.append(GeneDict[node])
		print templist
                geneList.append(templist)
        except nx.NetworkXException:
            return ("\nNo path exists between given genes.")
    return geneList

#gets rid of 5 genes that are not part of
#the bigger connected component
def Discard_Genes(listOfGenes):
    temp = []
    endResult = ""
    for gene in listOfGenes:
        if gene in AlreadyCreated:
	        temp.append(gene)
        else:
            endResult += (gene + " is not in the data source.\n")
    print endResult

    return temp